So, I totally forgot to post this earlier but PKHeX seems to have issues with the Ribbons obtained on a Pokemon. PKHeX flags incorrectly a Pokemon as illegal if it has the Gen 6 Contest Master Ribbons when they originate from older generations. As you can see on the picture of my Ribbon Mastered Latios (originated from Gen 3), it says that the ORAS Contest Master Ribbons are missing even though they are present on the Pokemon's description. The reason why I can say this is because when I compared it to a Greninja with the ribbons, it shows no issue. Any Pokemon from Gen 3/4/5/6 can obtain the ORAS Master Contest Ribbons, which is why it shouldn't be flagged as illegal.
Apart from this, I would like to add something about DUKING's trades (The Larvitar, Shuckle and Meditite you receive from DUKING in Pokemon XD: Gale of Darnkess), where PKHeX flags illegal the shiny versions of them when it isn't true as they can be RNG abused as long as you have a compatible SID. On this picture, you can see it reports it as a Mystery Gift mismatch. You can see proof of my RNG abused Larvitar here.
The last issue I would like to report involves Pokemon from my Japanese Colosseum. This is the name I picked in-game back when I started this save, however, PKHeX flags it as an invalid Word filter and makes any Pokemon I obtained from my Japanese Colosseum flagged incorrectly. I never edited the OT, so I have no idea on why this happened. I'm not sure what I could offer on this one, but I don't mind uploading my JPN colo save file in case it is needed.
Thanks everyone for your attention and your time in here. I might have some more bugs to report, but I may have forgotten about them. I appreciate your help on this and keep up the good work with PKHeX :D.